******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.2 (Release date: Sun Jan 29 10:33:12 2023 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= housekeeping.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ rpmF 1.0000 100 rpoZ 1.0000 100 mucS 1.0000 100 cds-GIU65890.1 1.0000 100 nrdR 1.0000 100 nusB 1.0000 100 dnaX 1.0000 100 umuD 1.0000 100 umuC 1.0000 100 cds-GIU65947.1 1.0000 100 cds-GIU65955.1 1.0000 100 cds-GIU65992.1 1.0000 100 cds-GIU66003.1 1.0000 100 cds-GIU66046.1 1.0000 100 cds-GIU66054.1 1.0000 100 cds-GIU66089.1 1.0000 100 coaX 1.0000 100 tsf 1.0000 100 rpsB 1.0000 100 mfd 1.0000 100 rpoC 1.0000 100 rpoB 1.0000 100 cds-GIU66145.1 1.0000 100 rplL 1.0000 100 rplJ 1.0000 100 rplA 1.0000 100 rplK 1.0000 100 nusG 1.0000 100 cds-GIU66165.1 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme housekeeping.fasta -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 3 -minw 6 -maxw 50 -objfun classic -minsites 2 -markov_order 0 model: mod= zoops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 6 maxw= 50 nsites: minsites= 2 maxsites= 29 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 2900 N= 29 sample: seed= 0 hsfrac= 0 searchsize= 2900 norand= no csites= 1000 Letter frequencies in dataset: A 0.236 C 0.239 G 0.259 T 0.266 Background letter frequencies (from file dataset with add-one prior applied): A 0.236 C 0.239 G 0.259 T 0.266 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAYNWAGCCCWARACGTNGKSGAAKSYTG MEME-1 width = 29 sites = 6 llr = 125 E-value = 1.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAYNWAGCCCWARACGTNGKSGAAKSYTG MEME-1 Description -------------------------------------------------------------------------------- Simplified A aa2258222238772::2:22288:2::2 pos.-specific C ::53:::587:::27:232:3:2::53:: probability G :::2:282:22232:a:28357:273:28 matrix T ::335::2::5:::2:83:5:2::3:78: bits 2.1 ** 1.9 ** * 1.7 ** * 1.5 ** * * * * ** Relative 1.3 ** ** * * ** * ** ** Entropy 1.0 ** *** * ** ** * *** *** (30.1 bits) 0.8 ** *** ** ****** * *** *** 0.6 *** *** ** ****** * ********* 0.4 *** *** ********* *********** 0.2 *** ************* *********** 0.0 ----------------------------- Multilevel AACCAAGCCCTAAACGTCGTGGAAGCTTG consensus TTT A G T GC TGC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAYNWAGCCCWARACGTNGKSGAAKSYTG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------- nrdR 68 5.37e-12 TACAGGGGGT AAAGAAGCCCTAACCGTCGTCAAAGGTTG TTCT cds-GIU65955.1 38 2.91e-11 TAGATGCGCA AACCAAGCCCGAGGCGTTGGGGCATGTTG CATGGGAATT cds-GIU66145.1 23 1.34e-10 AAAAATCCGA AATTTAGACCAAAAAGTGGTGGAGGCCTA AAAAGGTCGG cds-GIU65947.1 7 2.54e-10 TCGCAG AATCTGGTCGTAAACGTTCGCTAAGCTTG TCGCAAGGTT mucS 58 4.59e-10 CTTTTGCCTT AACTTAACACTAAACGTCGAAGAATACGG CGGGAGAAAA nusB 27 7.41e-10 CGATCAAAAG AACAAAGGCAAGGATGCAGTGGAAGCTTG CTTGACATTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAYNWAGCCCWARACGTNGKSGAAKSYTG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- nrdR 5.4e-12 67_[+1]_4 cds-GIU65955.1 2.9e-11 37_[+1]_34 cds-GIU66145.1 1.3e-10 22_[+1]_49 cds-GIU65947.1 2.5e-10 6_[+1]_65 mucS 4.6e-10 57_[+1]_14 nusB 7.4e-10 26_[+1]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAYNWAGCCCWARACGTNGKSGAAKSYTG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAYNWAGCCCWARACGTNGKSGAAKSYTG width=29 seqs=6 nrdR ( 68) AAAGAAGCCCTAACCGTCGTCAAAGGTTG 1 cds-GIU65955.1 ( 38) AACCAAGCCCGAGGCGTTGGGGCATGTTG 1 cds-GIU66145.1 ( 23) AATTTAGACCAAAAAGTGGTGGAGGCCTA 1 cds-GIU65947.1 ( 7) AATCTGGTCGTAAACGTTCGCTAAGCTTG 1 mucS ( 58) AACTTAACACTAAACGTCGAAGAATACGG 1 nusB ( 27) AACAAAGGCAAGGATGCAGTGGAAGCTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAYNWAGCCCWARACGTNGKSGAAKSYTG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 2088 bayes= 8.88736 E= 1.2e+000 208 -923 -923 -923 208 -923 -923 -923 -50 106 -923 33 -50 48 -64 33 108 -923 -923 91 182 -923 -64 -923 -50 -923 168 -923 -50 106 -64 -67 -50 180 -923 -923 -50 148 -64 -923 50 -923 -64 91 182 -923 -64 -923 150 -923 36 -923 150 -52 -64 -923 -50 148 -923 -67 -923 -923 195 -923 -923 -52 -923 165 -50 48 -64 33 -923 -52 168 -923 -50 -923 36 91 -50 48 95 -923 -50 -923 136 -67 182 -52 -923 -923 182 -923 -64 -923 -923 -923 136 33 -50 106 36 -923 -923 48 -923 133 -923 -923 -64 165 -50 -923 168 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAYNWAGCCCWARACGTNGKSGAAKSYTG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 6 E= 1.2e+000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.500000 0.000000 0.333333 0.166667 0.333333 0.166667 0.333333 0.500000 0.000000 0.000000 0.500000 0.833333 0.000000 0.166667 0.000000 0.166667 0.000000 0.833333 0.000000 0.166667 0.500000 0.166667 0.166667 0.166667 0.833333 0.000000 0.000000 0.166667 0.666667 0.166667 0.000000 0.333333 0.000000 0.166667 0.500000 0.833333 0.000000 0.166667 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.166667 0.166667 0.000000 0.166667 0.666667 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.166667 0.333333 0.166667 0.333333 0.000000 0.166667 0.833333 0.000000 0.166667 0.000000 0.333333 0.500000 0.166667 0.333333 0.500000 0.000000 0.166667 0.000000 0.666667 0.166667 0.833333 0.166667 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 0.000000 0.666667 0.333333 0.166667 0.500000 0.333333 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.166667 0.833333 0.166667 0.000000 0.833333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAYNWAGCCCWARACGTNGKSGAAKSYTG MEME-1 regular expression -------------------------------------------------------------------------------- AA[CT][CT][AT]AGCCC[TA]A[AG]ACGT[CT]G[TG][GC]GAA[GT][CG][TC]TG -------------------------------------------------------------------------------- Time 1.47 secs. ******************************************************************************** ******************************************************************************** MOTIF WMMHRHWBTMYGADHCVDRHSHGHKMSSHGWWMSHSVABBMGCGBTYT MEME-2 width = 48 sites = 8 llr = 189 E-value = 4.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif WMMHRHWBTMYGADHCVDRHSHGHKMSSHGWWMSHSVABBMGCGBTYT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 5544453::5::833:3455:3:415::3:445:3149:14::111:1 pos.-specific C :544:3133443314a4:13641315453:::34333:346191314: probability G 1:1:6:14:1:8:3::433:41915:651a1:15:54:53:6:641:1 matrix T 4:13:3548:6::44::413:3:33:::4:561151:133:3113668 bits 2.1 * 1.9 * * 1.7 * * 1.5 * * * * * Relative 1.3 ** * * * * * Entropy 1.0 * * * *** * * * *** * * * * * * (34.0 bits) 0.8 * * * *** * * * *** * * * * * ** 0.6 ** ** ***** * ** * *** *** * * *** ** 0.4 ** *** ****** **** ** * *** *** ** *** **** *** 0.2 ************* ************** ********** **** *** 0.0 ------------------------------------------------ Multilevel AAAAGATGTATGATCCCAAACCGAGAGCTGTTAGTGAAGCCGCGGTTT consensus TCCCACATCCCCCAT GTGCGA CTCCGA AACCACG CGAT C C sequence T T C GA AG T T T C C C TT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMMHRHWBTMYGADHCVDRHSHGHKMSSHGWWMSHSVABBMGCGBTYT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------------------ nusG 44 5.27e-16 GCGTCGCAGC AACCGAAGTATGAGCCGTAACCGCCCCCTGTTATTCAACTCGCGGTTT ACCATATAG umuC 10 1.06e-12 CGGCTGAGA ACAAGAATTATCCATCCATACCGATCGGTGAAGGTGATTGCGCGTTTT GGGGCGTCGT cds-GIU66003.1 34 1.30e-12 ACTTGGTAGT ACCCGTTGTCCGATACCTCACGCTGACGAGTTAGCGGAGTAGCGTTTA CGCAAACTTC rpoZ 11 6.39e-12 ATAGCCCAAA TATAACTTTGTGATCCATATGCGTGCGGTGGTTGAGAAGCCTCACTTT ATAGACTAGA cds-GIU66054.1 33 2.35e-11 TATTTGATTT GAGTGTTTTATCATTCCGAACTGAACGCAGTTACTGGAGGCGTTGCCT TTGGTCTGCT rpoC 36 2.95e-11 AAAAACTTAC TCAAACGCCCCGCACCAAACGTGCGAGGCGAAACAAGAGAAGCGCTCT TGCCCTCTGA rplA 51 1.08e-10 GCGCTGGTTC TAATAACGTCCGAGACGGGCCAGATACCCGAACCTTCACCATCGAATT AG mfd 15 3.22e-10 ACGGTGGGTT ACCCGATCCATGACTCGAGTGAGGGAGCGGTTCGCCCATCCCCCGGCG ATATCGGACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMMHRHWBTMYGADHCVDRHSHGHKMSSHGWWMSHSVABBMGCGBTYT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- nusG 5.3e-16 43_[+2]_9 umuC 1.1e-12 9_[+2]_43 cds-GIU66003.1 1.3e-12 33_[+2]_19 rpoZ 6.4e-12 10_[+2]_42 cds-GIU66054.1 2.4e-11 32_[+2]_20 rpoC 2.9e-11 35_[+2]_17 rplA 1.1e-10 50_[+2]_2 mfd 3.2e-10 14_[+2]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMMHRHWBTMYGADHCVDRHSHGHKMSSHGWWMSHSVABBMGCGBTYT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WMMHRHWBTMYGADHCVDRHSHGHKMSSHGWWMSHSVABBMGCGBTYT width=48 seqs=8 nusG ( 44) AACCGAAGTATGAGCCGTAACCGCCCCCTGTTATTCAACTCGCGGTTT 1 umuC ( 10) ACAAGAATTATCCATCCATACCGATCGGTGAAGGTGATTGCGCGTTTT 1 cds-GIU66003.1 ( 34) ACCCGTTGTCCGATACCTCACGCTGACGAGTTAGCGGAGTAGCGTTTA 1 rpoZ ( 11) TATAACTTTGTGATCCATATGCGTGCGGTGGTTGAGAAGCCTCACTTT 1 cds-GIU66054.1 ( 33) GAGTGTTTTATCATTCCGAACTGAACGCAGTTACTGGAGGCGTTGCCT 1 rpoC ( 36) TCAAACGCCCCGCACCAAACGTGCGAGGCGAAACAAGAGAAGCGCTCT 1 rplA ( 51) TAATAACGTCCGAGACGGGCCAGATACCCGAACCTTCACCATCGAATT 1 mfd ( 15) ACCCGATCCATGACTCGAGTGAGGGAGCGGTTCGCCCATCCCCCGGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMMHRHWBTMYGADHCVDRHSHGHKMSSHGWWMSHSVABBMGCGBTYT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 48 n= 1537 bayes= 6.72432 E= 4.1e+001 108 -965 -105 50 108 106 -965 -965 67 65 -105 -108 67 65 -965 -9 67 -965 127 -965 108 6 -965 -9 8 -94 -105 91 -965 6 53 50 -965 6 -965 150 108 65 -105 -965 -965 65 -965 123 -965 6 153 -965 167 6 -965 -965 8 -94 -5 50 8 65 -965 50 -965 206 -965 -965 8 65 53 -965 67 -965 -5 50 108 -94 -5 -108 108 6 -965 -9 -965 138 53 -965 8 65 -105 -9 -965 -94 175 -965 67 6 -105 -9 -91 -94 95 -9 108 106 -965 -965 -965 65 127 -965 -965 106 95 -965 8 6 -105 50 -965 -965 195 -965 67 -965 -105 91 67 -965 -965 123 108 6 -105 -108 -965 65 95 -108 8 6 -965 91 -91 6 95 -108 67 6 53 -965 189 -965 -965 -108 -965 6 95 -9 -91 65 -5 -9 67 138 -965 -965 -965 -94 127 -9 -965 187 -965 -108 -91 -94 127 -108 -91 6 53 -9 -91 -94 -105 123 -965 65 -965 123 -91 -965 -105 150 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMMHRHWBTMYGADHCVDRHSHGHKMSSHGWWMSHSVABBMGCGBTYT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 48 nsites= 8 E= 4.1e+001 0.500000 0.000000 0.125000 0.375000 0.500000 0.500000 0.000000 0.000000 0.375000 0.375000 0.125000 0.125000 0.375000 0.375000 0.000000 0.250000 0.375000 0.000000 0.625000 0.000000 0.500000 0.250000 0.000000 0.250000 0.250000 0.125000 0.125000 0.500000 0.000000 0.250000 0.375000 0.375000 0.000000 0.250000 0.000000 0.750000 0.500000 0.375000 0.125000 0.000000 0.000000 0.375000 0.000000 0.625000 0.000000 0.250000 0.750000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.125000 0.250000 0.375000 0.250000 0.375000 0.000000 0.375000 0.000000 1.000000 0.000000 0.000000 0.250000 0.375000 0.375000 0.000000 0.375000 0.000000 0.250000 0.375000 0.500000 0.125000 0.250000 0.125000 0.500000 0.250000 0.000000 0.250000 0.000000 0.625000 0.375000 0.000000 0.250000 0.375000 0.125000 0.250000 0.000000 0.125000 0.875000 0.000000 0.375000 0.250000 0.125000 0.250000 0.125000 0.125000 0.500000 0.250000 0.500000 0.500000 0.000000 0.000000 0.000000 0.375000 0.625000 0.000000 0.000000 0.500000 0.500000 0.000000 0.250000 0.250000 0.125000 0.375000 0.000000 0.000000 1.000000 0.000000 0.375000 0.000000 0.125000 0.500000 0.375000 0.000000 0.000000 0.625000 0.500000 0.250000 0.125000 0.125000 0.000000 0.375000 0.500000 0.125000 0.250000 0.250000 0.000000 0.500000 0.125000 0.250000 0.500000 0.125000 0.375000 0.250000 0.375000 0.000000 0.875000 0.000000 0.000000 0.125000 0.000000 0.250000 0.500000 0.250000 0.125000 0.375000 0.250000 0.250000 0.375000 0.625000 0.000000 0.000000 0.000000 0.125000 0.625000 0.250000 0.000000 0.875000 0.000000 0.125000 0.125000 0.125000 0.625000 0.125000 0.125000 0.250000 0.375000 0.250000 0.125000 0.125000 0.125000 0.625000 0.000000 0.375000 0.000000 0.625000 0.125000 0.000000 0.125000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMMHRHWBTMYGADHCVDRHSHGHKMSSHGWWMSHSVABBMGCGBTYT MEME-2 regular expression -------------------------------------------------------------------------------- [AT][AC][AC][ACT][GA][ACT][TA][GTC][TC][AC][TC][GC][AC][TAG][CTA]C[CGA][ATG][AG][ACT][CG][CAT]G[ACT][GT][AC][GC][CG][TAC]G[TA][TA][AC][GC][TAC][GC][AGC]A[GCT][CGT][CA][GT]CG[GCT]T[TC]T -------------------------------------------------------------------------------- Time 2.80 secs. ******************************************************************************** ******************************************************************************** MOTIF TTGAAATT MEME-3 width = 8 sites = 7 llr = 67 E-value = 1.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTGAAATT MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::97a:: pos.-specific C ::113::: probability G ::9::::: matrix T aa::::aa bits 2.1 * 1.9 ** *** 1.7 ** *** 1.5 **** *** Relative 1.3 ******** Entropy 1.0 ******** (13.8 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTGAAATT consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGAAATT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- cds-GIU66165.1 22 1.70e-05 GAAATCACCA TTGAAATT GAGGGTGAAG tsf 69 1.70e-05 CCGGTCCCGT TTGAAATT TTTGTGAACT cds-GIU66046.1 27 1.70e-05 GGACGGAGCC TTGAAATT AAGTCAGGCT cds-GIU66089.1 59 3.43e-05 AGGCGTTACT TTGACATT GGACATCGTC nusB 57 3.43e-05 GGAAGCTTGC TTGACATT GCTGGCCACC cds-GIU66003.1 89 5.00e-05 TTACGCAAAC TTCAAATT GGTT rpmF 9 6.73e-05 TTAATTGG TTGCAATT AGGGGCGCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGAAATT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-GIU66165.1 1.7e-05 21_[+3]_71 tsf 1.7e-05 68_[+3]_24 cds-GIU66046.1 1.7e-05 26_[+3]_66 cds-GIU66089.1 3.4e-05 58_[+3]_34 nusB 3.4e-05 56_[+3]_36 cds-GIU66003.1 5e-05 88_[+3]_4 rpmF 6.7e-05 8_[+3]_84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGAAATT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTGAAATT width=8 seqs=7 cds-GIU66165.1 ( 22) TTGAAATT 1 tsf ( 69) TTGAAATT 1 cds-GIU66046.1 ( 27) TTGAAATT 1 cds-GIU66089.1 ( 59) TTGACATT 1 nusB ( 57) TTGACATT 1 cds-GIU66003.1 ( 89) TTCAAATT 1 rpmF ( 9) TTGCAATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGAAATT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 2697 bayes= 8.42949 E= 1.8e+002 -945 -945 -945 191 -945 -945 -945 191 -945 -74 172 -945 186 -74 -945 -945 160 26 -945 -945 208 -945 -945 -945 -945 -945 -945 191 -945 -945 -945 191 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGAAATT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 1.8e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.857143 0.000000 0.857143 0.142857 0.000000 0.000000 0.714286 0.285714 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGAAATT MEME-3 regular expression -------------------------------------------------------------------------------- TTGA[AC]ATT -------------------------------------------------------------------------------- Time 3.90 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- rpmF 1.66e-02 8_[+3(6.73e-05)]_84 rpoZ 3.43e-08 10_[+2(6.39e-12)]_42 mucS 2.25e-06 57_[+1(4.59e-10)]_14 cds-GIU65890.1 8.04e-01 100 nrdR 1.20e-09 67_[+1(5.37e-12)]_4 nusB 3.73e-08 26_[+1(7.41e-10)]_1_[+3(3.43e-05)]_\ 36 dnaX 8.15e-01 100 umuD 5.91e-01 100 umuC 9.00e-09 9_[+2(1.06e-12)]_43 cds-GIU65947.1 2.37e-06 6_[+1(2.54e-10)]_65 cds-GIU65955.1 9.48e-08 37_[+1(2.91e-11)]_34 cds-GIU65992.1 1.74e-01 100 cds-GIU66003.1 4.75e-11 33_[+2(1.30e-12)]_7_[+3(5.00e-05)]_\ 4 cds-GIU66046.1 1.58e-02 26_[+3(1.70e-05)]_66 cds-GIU66054.1 2.27e-08 32_[+2(2.35e-11)]_20 cds-GIU66089.1 1.18e-02 58_[+3(3.43e-05)]_34 coaX 1.27e-01 100 tsf 2.67e-02 68_[+3(1.70e-05)]_24 rpsB 4.79e-01 100 mfd 7.60e-07 14_[+2(3.22e-10)]_38 rpoC 8.46e-08 35_[+2(2.95e-11)]_17 rpoB 5.87e-01 100 cds-GIU66145.1 5.49e-07 22_[+1(1.34e-10)]_49 rplL 4.47e-01 100 rplJ 4.05e-01 100 rplA 1.18e-07 50_[+2(1.08e-10)]_2 rplK 9.57e-01 100 nusG 3.05e-12 43_[+2(5.27e-16)]_9 cds-GIU66165.1 3.03e-03 21_[+3(1.70e-05)]_71 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************